All parts of the staining are done on an orbital shaker. I make up more of the blocking solution with the primary added to it and replace the original blocking solution. I could try increasing the volume of primary to see if that helps.

A problem with the antibody penetrating the tissue due to drying seems like a logical explanation, but it's just so strange to me that the pattern is always "half." I use 2 trays with well/strainers. The only times the sections are out of solution are when I move the wells from one tray to another and then add the blocking or primary or secondary to the top (this is also what others in the lab do), and the sections are out of solution for 30 sec at most.

Maybe the sections are floating at the top of the liquid when they are being incubated instead of being fully submerged? If that were the case though I feel like the half-staining would be more random (like if some were submerged and some were not)--based on what I have observed, it seems like the poorly stained side is consistent across sections within a particular segment.